rs1547531

Variant names:

• chr5-30796284-G-A
• rs1547531

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.808 in 151,926 control chromosomes in the GnomAD database, including 49,900 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (49900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122660 AN: 151810 Hom.: 49848 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.806

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.808 AC: 122771 AN: 151926 Hom.: 49900 Cov.: 31 AF XY: 0.809 AC XY: 60100 AN XY: 74246

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.807

Alfa AF: 0.782 Hom.: 21431

Bravo AF: 0.820

Asia WGS AF: 0.913 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.69
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1547531; hg19: chr5-30796391;